Thomas Kent
Local Journalism Initiative Reporter
Woolwich Observer
From soil microbes to drought maps, federal researchers are providing Canadian farmers with new tools to adapt.
Agriculture and Agri-Food Canada (AAFC) scientists are helping farmers and policymakers better understand the forces reshaping Canadian agriculture, from the microscopic life beneath their fields to large-scale drought patterns spreading across the country.
AAFC researchers are working to generate early indicators that can help producers respond more quickly to environmental stress, improve resilience, and make more informed management decisions.
One focus area is soil health, where AAFC microbiologist Dr. Lori Phillips uses molecular science to detect changes well before they show up in traditional soil tests.
Based at AAFC’s Harrow Research and Development Centre, Phillips studies how soil microbes – bacteria and fungi – respond to farming practices such as tillage, cover cropping, and reduced disturbance.
“Microbes are a little bit like the canaries in the coal mine,” Phillips told The Observer. “They respond to what we do to the soil much more rapidly than things like soil carbon or organic matter.”
Her team extracts DNA and RNA from soil samples to identify the microbial communities present and the functions they perform. Because microbes process nearly all soil nutrients, shifts in these communities can indicate whether soil health is improving or declining.
In recent AAFC field trials, Phillips’ team discovered that after only one year of perennial cover cropping, microbial activity related to nutrient cycling increased.
After five years, researchers noted significant changes in microbial communities and organic nitrogen levels, well before conventional soil indicators would usually show improvement.
“These tools let us see the direction the system is going in much sooner,” Phillips said. “That can save farmers years of waiting to find out whether a practice change is going to pay off.”
Soil microbes are essential for water infiltration, nutrient availability, disease control, and chemical breakdown. Soils with more biological diversity generally handle excess moisture and drought better, helping farms adapt to increasingly unpredictable weather.
Phillips said farmers often ask how long it takes for management changes to show results. This is especially true when early yield losses can occur as soils adjust.
“If you only look at yield in the first year, you might abandon a practice that’s actually setting you up for long-term resilience,” she said. “The microbes can tell us those benefits are coming.”
She said the research can also help inform government support programs and policy decisions by providing data on soil health indicators and management outcomes.
“When resources are limited, it’s important to know which practices give the biggest return in resilience and sustainability,” Phillips explained.
Phillips’ work is increasingly focused on what she calls the “interfaces of change”, that is, places where land use, climate, and ecosystems are shifting most rapidly.
As climate change pushes the boundaries of Canadian agriculture northward, new cropland is emerging in regions where farming has not traditionally occurred, including parts of Newfoundland, northern Ontario, Quebec, and the Yukon.
“When land is first cleared and put into agricultural production, there’s a window of time where management decisions really matter,” Phillips told The Observer. “Microbes can tell us how quickly those systems are changing and how much time we have to act.”
Her team is studying how soil microbial communities shift as forested land is converted to farmland, particularly nitrogen-cycling organisms, which can influence both soil fertility and greenhouse gas emissions. Understanding those early changes could help farmers and policymakers identify best practices before long-term problems develop.
“If we can get good practices in place at the start, that’s much easier than trying to change systems 20 years down the road,” Phillips said.
AAFC recently approved new funding to expand this work, with field projects in Newfoundland, Quebec, Ontario and the Yukon set to begin in early 2026.
Phillips is also examining how nutrients and soil microbes move beyond farm fields and into surrounding waterways. This is an issue of particular concern in southern Ontario, especially in the Region, where extensive tile drainage systems rapidly channel water, nitrogen, and phosphorus into drainage ditches and streams.
“What we’re finding is that it’s not just nutrients leaving the field,” she explained. “It’s also microbial communities that are capable of cycling those nutrients.”
Those microbes, she noted, could potentially play a role in mitigating downstream impacts such as algal blooms if appropriate in-ditch and riparian management strategies are in place.
By tracking how nutrients and microbes move through soils, ditches, streams, and larger water bodies, including the Great Lakes, researchers are beginning to identify patterns that could inform better water-quality protection strategies.
“It allows us to see how very different ecosystems are connected,” Phillips said. “Once you start seeing the spatial and temporal patterns, it begins to make sense as a whole system.”
Phillips emphasized that much of AAFC’s work is designed as public-interest research – generating knowledge that benefits society and the environment rather than commercial products – and plays a role that industry research often does not.
“This kind of research helps farmers understand not just what to do, but why,” she said. “That matters when you’re asking people to make changes on their farms.”
She added that, in the long term, publicly funded agricultural research provides the foundation for future innovation, even if its benefits are not immediately commercial.
“There’s a clear role for government research in this space,” Phillips said, adding that government research can also help inform future policy and on-farm support programs by identifying which practices deliver the greatest benefits for resilience and sustainability, especially in regions facing rapid environmental change.
